[3dem] Transitioning to PDBx/mmCIF and Extended PDB IDs

[Justin Flatt]

wwPDB strongly encourages all users to adopt the extended PDB ID format 
and transition to PDBx/mmCIF file format as soon as possible. This 
includes making changes to software; referring to structures by the full 
12-character ID in all communications; and encouraging your communities 
to do the same.

TRANSITIONING TO EXTENDED PDB IDS

As the PDB archive continues to expand, the four-character PDB accession 
codes (PDB IDs) are expected to be fully assigned before 2028. To 
support the growth of the archive, the wwPDB has extended the length of 
PDB IDs to 12 alphanumeric characters including "pdb_" prefix (e.g., 
"1abc" will become "pdb_00001abc", case insensitive) to improve text 
mining capabilities in the published literature. Users or journals will 
be able to parse/recognize PDB IDs using the prefix "pdb_". The prefix 
and zeros must be included in the extended PDB ID.

Once four-character PDB IDs are fully assigned, new entries will only 
receive extended PDB IDs; data will not be provided in the legacy PDB 
file format files.

Access further details, including a transition plan, example files, and 
supporting FAQs at wwPDB: Extended PDB ID With 12 Characters [1].

Users can adopt usage of extended PDB IDs for all PDB entries 
immediately using the _database_2.pdbx_database_accession data item in 
the PDBx/mmCIF formatted structure files.

For example:

  loop_
  _database_2.database_id
  _database_2.database_code
  _database_2.pdbx_database_accession
  _database_2.pdbx_DOI
  PDB 2HYV pdb_00002hyv 10.2210/pdb2hyv/pdb
  WWPDB D_1000038924 ? ?

NEW PDB DOI FORMAT

All existing PDB entries with four-character PDB IDs issued have DOI 
formatted as 10.2210/pdb[4-character_PDB_ID]/pdb that resolve to the 
corresponding wwPDB DOI landing page. For example, PDB entry 8y9m 
(pdb_00008y9m) has the DOI https://urldefense.com/v3/__https://doi.org/10.2210/pdb8y9m/pdb__;!!Mih3wA!D3jzMa-3QETF-pu4Z4tpzgYKujPB1FRQjSsFmBXE5rlloU165hwRprmqnP5DavSoTU6LE6cTiB6y_sTxQnth4mZW$  [2]. 
Importantly, this DOI will remain unchanged in the future.

When all 4-character PDB IDs have been exhausted, all new PDB entries 
will be issued extended PDB IDs issued and a NEW DOI formatted as 
10.2210/[Extended_PDB_ID]/pdb that will resolve to the corresponding 
wwPDB DOI landing page. For example, PDB entry "pdb_10001xyz" will have 
the DOI https://urldefense.com/v3/__https://doi.org/10.2210/pdb_10001xyz/pdb__;!!Mih3wA!D3jzMa-3QETF-pu4Z4tpzgYKujPB1FRQjSsFmBXE5rlloU165hwRprmqnP5DavSoTU6LE6cTiB6y_sTxQnfWRHbI$ .

TRANSITIONING TO PDBX/MMCIF FORMAT

To help users adopt extended PDB ID and PDBx/mmCIF file format, wwPDB 
offers an mmCIF User Guide [3] and software resources [4] such as mmCIF 
parsers and CIF Editor.

In addition, wwPDB will provide a Beta PDB Archive organized by extended 
PDB ID (including file naming, directories, and datablock naming) in 
early 2026. The current PDB archive organizes data files grouped by data 
type, e.g., coordinates, experimental data, assemblies, validation 
reports, etc.

A major change in the Beta PDB archive will be the re-organization of 
file directory at entry level, following the same file organization as 
the PDB Versioned Archive [5]. In other words, all the data files 
associated to an entry will be grouped together under its PDB ID 
(extended PDB ID) with two letter hash. Please watch wwPDB.org and 
community bulletin boards for announcements on the file organization for 
the Beta PDB archive later this year.

We recommend users fully adopt all of these these changes before the end 
of 2026. Early adoption will contribute to the long-term sustainability 
and interoperability of 3D biostructure data across the scientific 
community.

In particular, journals should begin adopting the Extended PDB ID format 
(in Text, Tables, and Data Availability Statements), updating links 
included in journal articles for PDB IDs to the wwPDB DOI landing page 
via CrossRef, and verifying software tools linked from a journal article 
(e.g., FirstGlance or Jsmol for 3D visualization) support of extended 
PDB IDs and PDBx/mmCIF.

Should you have any questions or require further assistance, please do 
not hesitate to contact us at info at wwpdb.org. We greatly appreciate your 
support and cooperation as we work together to enhance the future of 
structural data accessibility.

Links:
------
[1] https://urldefense.com/v3/__https://wwpdb.org/documentation/new-format-for-pdb-ids__;!!Mih3wA!D3jzMa-3QETF-pu4Z4tpzgYKujPB1FRQjSsFmBXE5rlloU165hwRprmqnP5DavSoTU6LE6cTiB6y_sTxQqDerY2M$ 
[2] https://urldefense.com/v3/__https://doi.org/10.2210/pdb8Y9M/pdb__;!!Mih3wA!D3jzMa-3QETF-pu4Z4tpzgYKujPB1FRQjSsFmBXE5rlloU165hwRprmqnP5DavSoTU6LE6cTiB6y_sTxQh7tbvf_$ 
[3] https://urldefense.com/v3/__https://mmcif.wwpdb.org/docs/user-guide/guide.html__;!!Mih3wA!D3jzMa-3QETF-pu4Z4tpzgYKujPB1FRQjSsFmBXE5rlloU165hwRprmqnP5DavSoTU6LE6cTiB6y_sTxQqZ05diA$ 
[4] https://urldefense.com/v3/__https://mmcif.wwpdb.org/docs/software-resources.html__;!!Mih3wA!D3jzMa-3QETF-pu4Z4tpzgYKujPB1FRQjSsFmBXE5rlloU165hwRprmqnP5DavSoTU6LE6cTiB6y_sTxQhno5qpS$ 
[5] https://urldefense.com/v3/__https://www.wwpdb.org/ftp/pdb-versioned-ftp-site__;!!Mih3wA!D3jzMa-3QETF-pu4Z4tpzgYKujPB1FRQjSsFmBXE5rlloU165hwRprmqnP5DavSoTU6LE6cTiB6y_sTxQk1Qkxsw$ 
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